Alignments for a candidate for fadA in Methylocapsa acidiphila B2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Methylocapsa acidiphila B2

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate WP_036255240.1 METAC_RS0102805 acetyl-CoA C-acyltransferase

Query= reanno::pseudo3_N2E3:AO353_25685
         (397 letters)



>NCBI__GCF_000427445.1:WP_036255240.1
          Length = 400

 Score =  548 bits (1412), Expect = e-160
 Identities = 271/389 (69%), Positives = 323/389 (83%)

Query: 6   DPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGL 65
           DPIVI SA RTP+GGFQG+ K L+AP+LGAAAI AAVER+G+  + ++E + GCVL+AG 
Sbjct: 10  DPIVIASAARTPIGGFQGDFKDLAAPRLGAAAIAAAVERSGLHPEDIDEAILGCVLTAGQ 69

Query: 66  GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNA 125
           GQAPARQAAL AGL  +  C T+NKMCGSGM+A +LAHD+L AGSA  +VAGGMESM+NA
Sbjct: 70  GQAPARQAALAAGLPAAAGCLTINKMCGSGMKAIMLAHDLLQAGSATAIVAGGMESMTNA 129

Query: 126 PYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAI 185
           PYLL+R R+GYRMGHG++LDHMFLDGLEDAY    LMG FAE CA+A  FTREAQD +A 
Sbjct: 130 PYLLERTRAGYRMGHGRLLDHMFLDGLEDAYGAHPLMGVFAESCAQAFQFTREAQDAYAT 189

Query: 186 ASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTV 245
           AS  RAQ+AI+DG+F  EI P+    GK +K+I  DEQP KAKLDKIA+LKPAF++GGTV
Sbjct: 190 ASLLRAQKAIRDGNFIDEIAPVAAPAGKAEKIILHDEQPLKAKLDKIAALKPAFKEGGTV 249

Query: 246 TAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLK 305
           TAANSSSISDGA AL+LMRRSEAEKRGL+PLA I  HA+ A  P  FP AP+GA++KL+ 
Sbjct: 250 TAANSSSISDGATALVLMRRSEAEKRGLRPLATIRAHASHAQAPDQFPTAPIGALRKLMD 309

Query: 306 KTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTL 365
           KTGW+L +V+LFE+NEAFAVV++  M +L +PH KVNVHGGACALGHPIGASGARI+ TL
Sbjct: 310 KTGWALRDVDLFEINEAFAVVAMAAMRELALPHEKVNVHGGACALGHPIGASGARIVATL 369

Query: 366 LSALRQKGLKRGVAAICIGGGEATAMAVE 394
           L+AL+  GLKRG AAICIGGGEATA+AVE
Sbjct: 370 LAALKTYGLKRGAAAICIGGGEATALAVE 398


Lambda     K      H
   0.318    0.133    0.378 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 512
Number of extensions: 16
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 397
Length of database: 400
Length adjustment: 31
Effective length of query: 366
Effective length of database: 369
Effective search space:   135054
Effective search space used:   135054
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_036255240.1 METAC_RS0102805 (acetyl-CoA C-acyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01930.hmm
# target sequence database:        /tmp/gapView.23257.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-126  408.2   9.4   1.9e-126  408.0   9.4    1.0  1  lcl|NCBI__GCF_000427445.1:WP_036255240.1  METAC_RS0102805 acetyl-CoA C-acy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000427445.1:WP_036255240.1  METAC_RS0102805 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.0   9.4  1.9e-126  1.9e-126       1     385 []      14     398 ..      14     398 .. 0.97

  Alignments for each domain:
  == domain 1  score: 408.0 bits;  conditional E-value: 1.9e-126
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               i +a+Rtpig ++g +k+l a  L+aa+i +++er+gl+pe+ide+ilG+vl+ag+++++aR+aalaag
  lcl|NCBI__GCF_000427445.1:WP_036255240.1  14 IASAARTPIGGFQGDFKDLAAPRLGAAAIAAAVERSGLHPEDIDEAILGCVLTAGQGQAPARQAALAAG 82 
                                               789*******99********************************************************* PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               lp     lt+n++C+Sg++A++la + ++aG a+++vaGG+Esm+++p+ll++   r+++++g+ +l d
  lcl|NCBI__GCF_000427445.1:WP_036255240.1  83 LPAAAGCLTINKMCGSGMKAIMLAHDLLQAGSATAIVAGGMESMTNAPYLLERT--RAGYRMGHGRLLD 149
                                               ****************************************************97..89*********** PP

                                 TIGR01930 139 qllkdl....vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk.. 201
                                               ++  d+      ++  mg+ Ae++a+ ++++Re qD+ya +S  +a+kAi++g+f dei pv  +    
  lcl|NCBI__GCF_000427445.1:WP_036255240.1 150 HMFLDGledaYGAHPLMGVFAESCAQAFQFTREAQDAYATASLLRAQKAIRDGNFIDEIAPVAAPAGka 218
                                               9999999998778999**********************************************9987788 PP

                                 TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270
                                               +k++ +De++  + +l+k+a Lkpafke  g tvtA+Nss+++DGA+al+lm ++ a++ gl+pla+i+
  lcl|NCBI__GCF_000427445.1:WP_036255240.1 219 EKIILHDEQPL-KAKLDKIAALKPAFKE-GG-TVTAANSSSISDGATALVLMRRSEAEKRGLRPLATIR 284
                                               88888888887.899***********96.68.7************************************ PP

                                 TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339
                                               ++a  +  p++++++p+ A +k+++k+g+ ++d+dl+EinEAFA++++a+++el+ l +ekvNv+GGA 
  lcl|NCBI__GCF_000427445.1:WP_036255240.1 285 AHASHAQAPDQFPTAPIGALRKLMDKTGWALRDVDLFEINEAFAVVAMAAMRELA-LPHEKVNVHGGAC 352
                                               *******************************************************.88*********** PP

                                 TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               AlGHP+GasGariv+tll +Lk  g k+G a++C+ggG ++A+ +e
  lcl|NCBI__GCF_000427445.1:WP_036255240.1 353 ALGHPIGASGARIVATLLAALKTYGLKRGAAAICIGGGEATALAVE 398
                                               ******************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (400 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.91
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources